title: Single cell analysis of lymph node tissue from HIV-1 infected patients reveals that the majority of CD4+ T-cells contain one HIV-1 DNA molecule.
abstract: Genetic recombination contributes to the diversity of human immunodeficiency virus (HIV-1). Productive HIV-1 recombination is, however, dependent on both the number of HIV-1 genomes per infected cell and the genetic relationship between these viral genomes. A detailed analysis of the number of proviruses and their genetic relationship in infected cells isolated from peripheral blood and tissue compartments is therefore important for understanding HIV-1 recombination, genetic diversity and the dynamics of HIV-1 infection. To address these issues, we used a previously developed single-cell sequencing technique to quantify and genetically characterize individual HIV-1 DNA molecules from single cells in lymph node tissue and peripheral blood. Analysis of memory and naïve CD4(+) T cells from paired lymph node and peripheral blood samples from five untreated chronically infected patients revealed that the majority of these HIV-1-infected cells (>90%) contain only one copy of HIV-1 DNA, implying a limited potential for productive recombination in virus produced by these cells in these two compartments. Phylogenetic analysis revealed genetic similarity of HIV-1 DNA in memory and naïve CD4(+) T-cells from lymph node, peripheral blood and HIV-1 RNA from plasma, implying exchange of virus and/or infected cells between these compartments in untreated chronic infection.
authors.affiliation: Department of Microbiology, Tumor and Cell-biology, Karolinska Institutet, Solna, Sweden. Lina.josefsson@ki.se
authors.forename: Lina
authors.initials: L
authors.lastname: Josefsson
authors.forename: Sarah
authors.initials: S
authors.lastname: Palmer
authors.forename: Nuno R
authors.initials: NR
authors.lastname: Faria
authors.forename: Philippe
authors.initials: P
authors.lastname: Lemey
authors.forename: Joseph
authors.initials: J
authors.lastname: Casazza
authors.forename: David
authors.initials: D
authors.lastname: Ambrozak
authors.forename: Mary
authors.initials: M
authors.lastname: Kearney
authors.forename: Wei
authors.initials: W
authors.lastname: Shao
authors.forename: Shyamasundaran
authors.initials: S
authors.lastname: Kottilil
authors.forename: Michael
authors.initials: M
authors.lastname: Sneller
authors.forename: John
authors.initials: J
authors.lastname: Mellors
authors.forename: John M
authors.initials: JM
authors.lastname: Coffin
authors.forename: Frank
authors.initials: F
authors.lastname: Maldarelli
mesh_terms: D000328:Adult; D015496:CD4-Positive T-Lymphocytes / Q000378:metabolism* / Q000821:virology; D002908:Chronic Disease; D004279:DNA, Viral / Q000235:genetics / Q000378:metabolism*; D016679:Genome, Viral; D015658:HIV Infections / Q000235:genetics / Q000378:metabolism*; D015497:HIV-1 / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D008198:Lymph Nodes / Q000378:metabolism* / Q000821:virology; D008297:Male; D010802:Phylogeny
chemical_list: D004279:DNA, Viral